rs9508456

chr13-29442225-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001033602.4(MTUS2):c.3184+2176C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,040 control chromosomes in the GnomAD database, including 7,957 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.30 (7957 hom., cov: 32)
• Consequence: MTUS2 NM_001033602.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370

Genes affected

MTUS2 (HGNC:20595): (microtubule associated scaffold protein 2) Enables microtubule binding activity and protein homodimerization activity. Part of nucleus. Colocalizes with centrosome and cytoplasmic microtubule. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTUS2	NM_001033602.4	c.3184+2176C>T		intron_variant		ENST00000612955.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTUS2	ENST00000612955.6	c.3184+2176C>T		intron_variant		5	NM_001033602.4
MTUS2	ENST00000380808.6	c.121+2176C>T		intron_variant		1		P1
MTUS2	ENST00000542829.1	c.-150+13329C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45531 AN: 151922 Hom.: 7955 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.351

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.299 AC: 45530 AN: 152040 Hom.: 7957 Cov.: 32 AF XY: 0.296 AC XY: 22010 AN XY: 74294

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.348

Alfa AF: 0.385 Hom.: 15961

Bravo AF: 0.296

Asia WGS AF: 0.264 AC: 925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.32
Dann	Benign	0.56

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9508456; hg19: chr13-30016362;